When Energy Minimization Doesn’t Converge: What It Means and What to Do

Energy minimization is one of the most common steps performed in molecular modeling workflows. Whether you’re about to run a molecular dynamics simulation or preparing a system for docking, minimizing the system helps eliminate steric clashes and unrealistic geometries. But what happens when this step doesn’t fully converge?

If you’ve used the GROMACS Wizard Extension in SAMSON and find that your energy minimization run reaches the maximum number of steps without hitting your force tolerance, you’re not alone. This situation does not necessarily mean your project is broken, but it may signal a need for further action.

How to Check Convergence

When energy minimization completes, two key metrics determine whether the run was successful:

  • Potential energy (Epot) — This should be negative. For a protein in water, it’s typically on the order of 105 to 106 (depending on system size).
  • Maximum force (Fmax) — Defined by the emtol parameter, this is the threshold the minimization hopes to reach. If your minimization ends with a Fmax higher than the target (e.g., 1000 kJ mol-1 nm-1), convergence was not achieved.

You can check these values in the Output window after the run:

Output

Why Non-Convergence Happens

There are multiple reasons why your system might not minimize fully:

  • The system may be too strained — e.g., bad contacts, overlapping atoms, or unusual torsions.
  • The emtol value is too strict for your initial structure.
  • The number of steps allowed is insufficient to reach tolerance.
  • Your minimization parameters may not be optimal (e.g., integrator choice, step size).

What You Can Do

If your minimization did not converge but the potential energy is reasonable, you don’t necessarily need to start over. You can try one or more of these approaches:

  • Increase number of steps — Allow more iterations to reach the target force.
  • Reduce step size — Slower steps might allow the system to settle more gently.
  • Check for structural issues — Visual inspection in SAMSON can reveal steric clashes or missing atoms.
  • Modify minimization parameters — Access full GROMACS parameters by clicking on the All… button in the Minimize tab.

Advanced parameters

Should You Worry?

Not always. If Fmax is only slightly above the threshold and your structure looks reasonable, you may be able to proceed to the next simulation step. But if the discrepancy is large — or if the plot of potential energy levels off too early — some further troubleshooting is recommended.

What’s Next?

The GROMACS Wizard makes it easy to re-launch minimization using previous output, save and load parameters, and compare results. You can identify the issue incrementally without changing your broader project setup. To learn more, check out the original Energy Minimization documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net

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